Merge branch 'tisaac/dm-locate-points-sf'

* tisaac/dm-locate-points-sf:
Plex: missed in IS
DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

Merge branch 'sanderarens/fix-plex-neumann-bc'

* sanderarens/fix-plex-neumann-bc:
SNES ex77: Test now passing - Fixed memory leak - Use parser for numeric output
SNES ex77: Added test from Sande

Merge branch 'sanderarens/fix-plex-neumann-bc'

* sanderarens/fix-plex-neumann-bc:
SNES ex77: Test now passing - Fixed memory leak - Use parser for numeric output
SNES ex77: Added test from Sander - Does not work yet
SNES ex77: add small penalty term to Lagrangian density. This speeds up the linear solver convergence a lot and also allows for larger pressure loadings.
SNES ex62: Fixed output for proper block sizes
DM: pass down block size to subIS when creating a subDM.
SNES ex77: delete some unused variables.
SNES ex77: call DMPlexLabelComplete for correct Dirichlet bc's.
SNES+Plex: Add checks for valid IS after calls to DMLabelGetStratumIS.
SNES ex77: check if IS from DMGetStratumIS is a valid pointer as it can be NULL if used in parallel.
SNES: Add ex77: nonlinear elasticity with pressure loading
Plex: R should be a proper rotation from \hat z to n
SNES+Plex: Allow for multiple label values per boundary condition in BdResidual/BdJacobian
SNES+Plex: Fix the dimensions in BdResidual/BdJacobian

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Merge branch 'tisaac/fix-static-analysis-warnings'

* tisaac/fix-static-analysis-warnings:
Add missing CHKERRQ
Address static analysis warnings

Fixes for issues found with clang static analyzer,
mostly set but unused variables

Time: 1 hour

Address static analysis warnings

SNES+Plex: Add checks for valid IS after calls to DMLabelGetStratumIS.

SNES+Plex: Allow for multiple label values per boundary condition in BdResidual/BdJacobian

SNES+Plex: Fix the dimensions in BdResidual/BdJacobian

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping

DMLocatePoints: change output from an IS to a PetscSF, and allow initial guesses.

A PetscSF is a more natural return value from DMLocatePoints() because:
- In the event that the mesh has overlapping cells, it's clearer which
in which process/cell the point is located.
- A natural next step after DMLocatePoints() is to send each point to
its cell for some local computation. With a PetscSF this is easy with
PetscSFGatherBegin()/PetscSFGatherEnd().

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Update SNESMonitorSetFromOptions() to use PetscViewerAndFormat and hence no longer
have too many PetscViewerPushFormat()

Time: .5 hours

Merge branch 'barry/fix-private-functions'

const fixes for win32 warnings - related to 081a2d76edd0f29fad78624936ea4a95a96da0e2

More decreasing visibility of symbols from outside libraries
Also fix a few bugs related to having multiple PETSc libraries

Plex+SNES: Must assembly Jac and JacP

SNES+Plex: Do not calculate BdResidual/BdJacobian for FV

Plex: Convert dmAux to plex in DMPlexComputeJacobian_Internal()

DM+SNES/TS: Fixed caching of Plex

Plex+FVM: correct counting of fluxes

SNES+Plex: added DMPlexSetSNESLocalFEM()

Plex+SNES: remote Dirichlet bcs from residual when printing

Even though we're handling Dirichlet BC's in DMLocalToGlobal, for
debugging purposes it's helpful to display local residuals without the
v

Plex+SNES: remote Dirichlet bcs from residual when printing

Even though we're handling Dirichlet BC's in DMLocalToGlobal, for
debugging purposes it's helpful to display local residuals without the
values that will be removed.

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Plex+SNES:always use ADD_ALL_VALUES when summing FEM element matrices

The problem is that a dof being constrained no long means just a bc dof:
it could also mean a hanging constraint. In that case t

Plex+SNES:always use ADD_ALL_VALUES when summing FEM element matrices

The problem is that a dof being constrained no long means just a bc dof:
it could also mean a hanging constraint. In that case that dof's
contribution can't be treated as just zero: it must be summed (via the
hanging constraint) into the residual. The stripping of dirichlet
constraints is handled by DMLocalToGlobal().

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Plex: try to handle boundary conditions early

SNES+Plex: Added dynamic Jacobian, dF/du_t, to assembly

added a todo note for something to fix eventually

DMP4est/DMPlex: Share DMSNES/DMTS information when converting

This includes "A", "dmAux" and "dmCh" for now.